Cell Biology Animation

00:00:16.00 Hello, my name is Janet Iwasa, 00:00:18.09 and I am an animator at Harvard Medical School. 00:00:20.17 I'll be talking to you today 00:00:22.07 about some of the reasons I first got interested 00:00:24.06 in animation and the ways I think animation can really give back 00:00:27.18 to the research community. 00:00:29.11 So this animation of kinesin was really one of the first 00:00:32.23 things that I saw that really got me interested 00:00:35.00 in animation. I remember I was about a first or second 00:00:38.14 year graduate student in Dyche Mullins' lab, 00:00:40.24 studying the actin cytoskeleton at the time. 00:00:42.11 And I remember looking at this animation and thinking, why aren't we all doing this? 00:00:47.08 Why are we relying on these oversimplified static illustrations 00:00:52.05 when we can really be doing something like this which shows dynamics 00:00:55.15 and a lot of things way more accurately 00:00:57.05 than we currently are. 00:00:58.13 So within a year I started taking animation courses 00:01:02.00 at a local university and also started doing animations 00:01:05.15 of some of the processes that my lab was studying. 00:01:07.23 So all of my animations are really a close collaboration between myself and the people who are 00:01:13.12 doing the research, and there's a lot of real 00:01:15.25 back and forth that goes on 00:01:18.08 in the process of creating these animations. We go through 00:01:20.13 many, many iterations and change things like color 00:01:23.15 and dynamics, and in this case, the number of filaments, 00:01:26.04 how fast they should be depolymerizing and polymerizing. 00:01:28.15 And so it really is this great collaborative process. 00:01:32.00 Animations, it is really a pretty steep learning curve 00:01:36.03 to learning animations, and it was also...each animation really took me 00:01:39.25 quite a long time, especially at the beginning, 00:01:41.29 but I found that I really loved the process. 00:01:44.01 I loved sitting down with my labmates and trying to figure out what 00:01:48.07 these kind of processes should look like visually. 00:01:51.16 And I also found that it could really give back to the research 00:01:53.05 quite a bit. So, when you are creating an animation, 00:01:55.22 you are really grappling with a lot of issues that don't necessarily 00:01:58.10 come up by any other means. 00:02:00.28 For example, you have to think about not only stoichiometry, 00:02:03.13 but also dynamics and crowding, 00:02:05.17 things that may not come up if you are really creating 00:02:07.23 these very simple illustrations. 00:02:09.15 So towards the end of graduate school 00:02:12.17 I became interested in trying to look for opportunities 00:02:15.12 that I might be able to do animation as a postdoctoral fellow. 00:02:18.08 And I was really lucky to find an opportunity that was offered by the National Science Foundation 00:02:23.02 called the Discovery Core. 00:02:25.11 And so, as a Discovery Core fellow, I worked for two years with Jack Szostak 00:02:30.03 at Mass General Hospital and the Museum of Science in Boston 00:02:33.18 to create a multimedia exhibit on the origins of life. 00:02:36.00 And this used a number of animations that 00:02:38.20 explored ideas around the RNA World hypothesis 00:02:42.05 as well as some ideas of what the early Earth might have looked like. 00:02:45.04 So many of these animations really served a dual purpose. 00:02:49.05 First they were incorporated into a multimedia exhibit that included 00:02:52.15 a website as well as a kiosk on the museum floor 00:02:57.11 that is currently there right now, 00:02:59.00 as well as a number of live presentations that I gave at the Museum of Science. 00:03:05.09 And they were also used by researchers in the lab 00:03:08.07 to talk about their science to other researchers 00:03:11.02 And what we found was that just by altering the context, as well as 00:03:14.12 the narration for these animations, you could really 00:03:16.29 use the same animations for two different audiences. 00:03:19.15 I also grew quite a lot as an animator during this 00:03:23.14 time, so I was really lucky to be able to take kind of a 00:03:27.15 crash course in animation in Hollywood for the summer before my postdoc started. 00:03:32.16 And this really allowed me to hit the ground running. 00:03:35.00 And I also found that there are a lot of tricks that you have to use in animation to 00:03:38.14 create molecular animations. So a lot of the animation packages that we use today 00:03:43.01 are really more for animating things like Buzz Lightyear 00:03:45.15 rather than molecules like actin. 00:03:47.14 So for example for this animation, 00:03:49.12 I used cloth simulation to try to create a simulation of RNA folding. 00:03:55.09 So what I also found was that animation could be a 00:03:58.18 great handle that the public could use to try to grasp 00:04:01.12 and understand complex molecular ideas. 00:04:04.04 So animation can really eliminate the need for jargon 00:04:07.29 in many cases and is also quite approachable. 00:04:10.10 And so for these kinds of reasons I think animation 00:04:13.16 can really be a great tool to try to make a positive impact 00:04:18.16 on science education, as well as the public perception of science 00:04:22.20 and ultimately, and hopefully, science policy. 00:04:25.15 After my postdoc, I started working at Harvard Medical School in the Cell Biology department. 00:04:31.15 One of the things that I am really interested in understanding 00:04:34.09 is how animation can be used by researchers to better explore and communicate 00:04:39.13 their kind of molecular hypotheses. 00:04:42.11 And so this is an example of this kind of project, this is an animation 00:04:46.06 clathrin mediated endocytosis 00:04:48.10 that I worked on with Tom Kirchhausen. 00:04:50.10 And what I found was that animations can really synthesize a 00:04:53.18 great deal of information, including...you can include molecular structures 00:04:59.09 from crystal structures and EM sources, 00:05:02.21 as well as you can include dynamics from light microscopy data, 00:05:06.24 as well as how protein-protein interactions 00:05:09.14 that are derived from genetics and biochemical experiments. 00:05:12.06 And another thing to note is that these kind of animations 00:05:17.01 are really kind of a visualization of a hypothesis. 00:05:19.10 So they may not, everything in the animation may not be completely supported by 00:05:25.01 experimental evidence, while other things may be, 00:05:27.14 and I think that's the same for any kind of hypothesis. 00:05:29.19 I also found that animations can really be 00:05:34.03 quite interesting for researchers, so the process of 00:05:36.23 creating an animation really makes you, as I mentioned before, 00:05:39.26 grapple with different issues that may not come up 00:05:41.22 when you are making other types of illustrations 00:05:44.15 so it is really kind of putting together a three dimensional 00:05:47.13 or a four dimensional puzzle. And by manipulating these different pieces you can really come up with 00:05:51.17 a lot of different ideas that 00:05:53.09 may not come up otherwise. 00:05:55.06 And I think for that reason, 00:05:57.16 these kind of animations and animation tools 00:05:59.28 may be able to really give back to research 00:06:02.12 and the research process. 00:06:04.02 So this final project that I would like to talk to you about 00:06:07.01 is a project that I am working on with Sam Reck-Peterson 00:06:10.00 at Harvard Medical School. Her lab is interested in 00:06:12.11 understanding the motor protein dynein and how 00:06:15.04 it walks along microtubules. 00:06:16.14 So as you might imagine this is a really 00:06:18.12 three dimensional and dynamic process. 00:06:20.15 And so using a 2D illustration such as this one really can be of limited utility. 00:06:26.29 when thinking about these kinds of problems. 00:06:29.03 So what we did together was to create a 3-dimensional 00:06:31.27 model of dynein that the lab could manipulate and move around 00:06:37.00 and really kind of use to explore the molecule in ways that they really 00:06:41.10 weren't able to before. 00:06:43.08 So really the goal of this project wasn't to create a finished and polished 00:06:47.02 animation, but really to create a new tool 00:06:49.15 that the lab could use to better study this process. 00:06:52.13 And using these kind of models, you can really start to 00:06:55.14 visualize the walk cycle of dynein, for example. 00:06:58.29 And each person in the lab, you can imagine, might have a different idea 00:07:02.11 of how this happens, and you can also start to try to predict 00:07:05.02 what might happen if, for example, you mutated the protein, or you put it in 00:07:08.19 to different conditions. And you can compare those things side by side 00:07:11.05 and potentially start designing experiments around these kinds of ideas. 00:07:15.21 And finally I wanted to leave you with a list of resources 00:07:20.10 that I hope might be useful for those of you who are interested 00:07:23.02 in learning more about animation. 00:07:25.01 The first is my website at Harvard Medical School 00:07:27.04 where you can download many of the animations that I showed you today 00:07:30.12 as well as new animations and new projects as they come up. 00:07:34.19 The second link here is called molecularmovies.org, which is 00:07:38.13 a really excellent resource. It has a gallery 00:07:41.09 of animations that you can download, a number of tutorials specific for molecular animation. 00:07:46.18 And there's also, in the past few years, been a number of 00:07:50.13 efforts to try to create new toolkits within 00:07:53.07 animation programs that can be used by researchers 00:07:55.10 to more easily upload and manipulate molecules. 00:07:59.15 And so this includes Molecular Maya, which is available at molecularmovies.org, 00:08:05.01 And this is for the program Maya. 00:08:06.18 There's also EPMV, which is available for Cinema4D, Maya, and Blender. 00:08:11.15 And there's also BioBlender, which is a tool kit for Blender. 00:08:14.08 So I really encourage you to take a look at some of these websites 00:08:18.06 if you are interested in learning more, and also feel free to contact me as well. 00:08:21.24 And also keep in mind that many of the software 00:08:26.02 that is out there you can download an educational version 00:08:29.04 and start exploring these animation tools for pretty much no cost. 00:08:34.01 And so that is something you also might consider doing as well. 00:08:37.02 Thank you.

Talk Overview

Janet Iwasa recalls the animation that first led her to realize how much more information can be included in an animation compared to a static image. She explains that cell biology animation can provide a visualization of a hypothesis and bring together structural data, protein-protein interactions and dynamic information in a process that often helps researchers refine their models.

Speaker Bio

While completing her PhD in cell biology at the University of California, San Francisco, Janet Iwasa began taking classes in animation. She honed her skills as a molecular animator during her post-doctoral fellowship and she has since joined forces with researchers to make animations of various biological processes. Iwasa joined the faculty at Harvard Medical… Continue Reading

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About Us

This material is based upon work supported by the National Science Foundation and the National Institute of General Medical Sciences under Grant No. MCB-1052331.

Any opinion, finding, conclusion, or recommendation expressed in these videos are solely those of the speaker and do not necessarily represent the views of iBiology, the National Science Foundation, the National Institutes of Health, or other iBiology funders.